---
name: "Bio::CodonUsage::IO"
section: "3pm"
platform: "linux"
package: "libbio-perl-perl"
version: "1.7.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::CodonUsage::IO"
---

# Bio::CodonUsage::IO(3pm)

for reading and writing codon usage tables to file

## NAME

Bio::CodonUsage::IO - for reading and writing codon usage tables to file

## SYNOPSIS

```
  use Bio::CodonUsage::IO;
  ## read in a codon usage file
  my $io = Bio::CodonUsage::IO->new(-file => "in");
  my $cut = $io->next_data();
  ## write it out again
  my $out = Bio::CodonUsage::IO->new(-file => ">out");
  $out->write_data($cut);
```

## DESCRIPTION

This class provides standard IO methods for reading and writing text files of codon usage tables. These tables can initially be retrieved using Bio::DB::CUTG. At present only this format is supported for read/write.

Reading a CUTG will return a Bio::CodonUsage::Table object.

## SEE ALSO

Bio::Tools::CodonTable,  Bio::WebAgent, Bio::CodonUsage::Table, Bio::CodonUsage::IO

## FEEDBACK

### Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists.  Your participation is much appreciated.

```
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
```

### Support

Please direct usage questions or support issues to the mailing list:

*bioperl-l@bioperl.org*

rather than to the module maintainer directly. Many experienced and  reponsive experts will be able look at the problem and quickly  address it. Please include a thorough description of the problem  with code and data examples if at all possible.

### Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution.  Bug reports can be submitted via the web:

```
  https://github.com/bioperl/bioperl-live/issues
```

## AUTHORS

Richard Adams, Richard.Adams@ed.ac.uk

## APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a \_

### new

```
 Title  : new
 Usage  : my $io = Bio::CodonUsage::IO->new(-file => "CUTfile");
 Purpose: To  read/write a Bio:CodonUsage::Table object
 Returns: A  Bio:CodonUsage::IO object
 Args   : a file or file handle
```

### next\_data

```
 Title  : next_data
 Usage  : my $cut = $io->next_data();
 Purpose: To  obtain a Bio:CodonUsage::Table object
 Returns: A  Bio:CodonUsage::Table object
 Args   : none
```

### write\_data

```
 Title  : write_data
 Usage  : $io->write_data($cut);
 Purpose: To  write a CUT to file
 Returns: void
 Args   : a Bio::CodonUsage::Table object reference
```